SimBiology

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Hi, Could someone explain me how I can use the sundials solver (CVODE), through my use of simBiology toolbox ? I know ODE solvers of Matlab and I used to use ODE15s. However, the latter fails in integration of stiff problems. So, I tried to use CVODE solver. The same issue occurs (if you are interested to know more about that please see my post on sundials forum : http://sundials.2283335.n4.nabble.com/force-the-CVODE-solver-to-continue-despite-the-error-test-failed-repeatedly-or-with-h-hmin-td4655576.html ). So, I ended up with the following troubleshooting solution being suggested for the very same solver included in SimBiology package ( https://nl.mathworks.com/help/simbio/ug/troubleshooting-simulation-errors.html ). Here you can see that they talk about two options of MaximumNumberOfLogs and MaximumWallClock, the use of which can help to avoid this problem. So, as I can not find these two options in CVODE directly downloaded from https://computation.llnl.gov/projects/sundials/sundials-software , I thought maybe these two options are only available in the SimBiology. Now, the problem is the following : there is no enough information/tutorial on this tool. How I can chage the following line to make use of SimBiology ? [T,Y]=ode15s(@source_terms,[0 tend],yinitial,options); I appreciate a lot your help, Best regards, Mary

Hi Everyone, I have a large stiff reaction network in Simbiology, which runs smoothly in R2010a with ode15s solver. I tested the code in R2012b and R2013a where the ode solver fails (all of them). A "very detailed" error message says: Error using SBCompiler.SimulationObject/simulate Integration Tolerance Not Met. If I export this model into SBML and back to matlab as an ODE function (calling ode15s() function), it runs without a problem in R2013a (using default ODE 15s settings). I was wondering is there any way to change the relTol, absTol settings for Simbiology simulations (configset obj)? It seems that way the (absolute/relative) tolerance settings for ode15s() and Simbiology's ode15s call are different. Thanks!